SART1 RNA-Seq in HepG2

General Information


RBP	SART1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SART1-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR505NDV
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR400YKV
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	SART1-BGHcLV22-49
Rep2	SART1-BGHcLV22-50
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	73.0
Rep2_qPCR	74.0
Rep1_WB	90.5
Rep2_WB	84.8
Antibody Cat#	A301-422A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB301DST
Status	Released
Project	ENCODE4
ID	48

Experiment Information (Status: Released)

	BGHcLV22-49	BGHcLV22-50
idx	642	643
TRCN#_or_BGC#	BGC#0000539	BGC#0000539
shRNA_or_gRNA_sequence	TATGGCCTTGCGACAGCGAG	TATGGCCTTGCGACAGCGAG
PAM	AGG	AGG
Name	SART1_96	SART1_96
Sample_ID	BGHcLV22-49	BGHcLV22-50
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	SART1	SART1
qPCR_result	73.0	74.0
Ave_qPCR	73.5
RT-qPCR_primer-F	TTTGGTGTCAGCACTCTGGT
RT-qPCR_primer-R	TTCTCGGAAGGAATCAATGG
protein_conc	2806	3056
WB_result	90.5	84.8
Ave_WB	87.7
WB_DONE_date	9/14/20	jess
MW	90.3kDa
IP	Rabbit / I
antibody_Cat#	A301-422A	LOT# 1
Antibody DCC ID	ENCAB301DST
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	6797	6798

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SART1	Product_ID: A301-422A Lot_ID: 1 Source: Bethyl Labs Target Name: SART1-human

Experiment Status

	BGHcLV22-49	BGHcLV22-50
Sample_ID	BGHcLV22-49	BGHcLV22-50
Sample Name
Sample Name	SART1-BGHcLV22-49	SART1-BGHcLV22-50
RBP	SART1	SART1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7389	7390

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-49	BGHcLV22-50
Sample #	25	26
Sample Name	SART1-BGHcLV22-49	SART1-BGHcLV22-50
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	296	301
Peak_Molarity	42.00	128.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/A4.png	DNA_Library_set46/set1/B4.png
RIN	9.4	9.6
libSample_RNA_Well	RNA_Library_set46/set1/A12.png	RNA_Library_set46/set1/B12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-49	BGHcLV22-50
RBP	SART1	SART1
Batch_ID	BGHcLV22	BGHcLV22
WB_result	90.500	84.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1400	1401

Sequencing Information

	BGHcLV22-49	BGHcLV22-50
Sample_ID	BGHcLV22-49	BGHcLV22-50
Sample Name	SART1-BGHcLV22-49	SART1-BGHcLV22-50
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	161,751,338	115,074,644
total_aligned_reads	125,196,624	100,729,622
unique_aligned_reads	117,600,240	94,767,316
percent_uniqueAligned	0.72704	0.82353
correlation_replicates	0.996894	0.996894
spikein_reads	117,138	53,398
percent_spikeins	0.00072	0.00046
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	506	507

Data Submission Information

	BGHcLV22-49	BGHcLV22-49	BGHcLV22-49	BGHcLV22-49	BGHcLV22-49	BGHcLV22-49	BGHcLV22-50	BGHcLV22-50	BGHcLV22-50	BGHcLV22-50
ENCODE_alias	brenton-graveley:SART1-BGHcLV22	brenton-graveley:SART1-BGHcLV22-49	brenton-graveley:L-SART1-BGHcLV22-49	brenton-graveley:SART1-BGHcLV22-49_ACTAAGAT+CCGCGGTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SART1-BGHcLV22-49_ACTAAGAT+CCGCGGTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SART1-BGHcLV22-HepG2	brenton-graveley:SART1-BGHcLV22-50	brenton-graveley:L-SART1-BGHcLV22-50	brenton-graveley:SART1-BGHcLV22-50_GTCGGAGC+TTATAACC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SART1-BGHcLV22-50_GTCGGAGC+TTATAACC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR400YKV	ENCBS046YDD	ENCLB688WVQ	ENCFF793KMC	ENCFF703KJU	ENCSR505NDV	ENCBS731VZI	ENCLB182BIN	ENCFF823IRO	ENCFF739NKQ
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV22-49	BGHcLV22-49	BGHcLV22-49	BGHcLV22-49	BGHcLV22-49	BGHcLV22-49	BGHcLV22-50	BGHcLV22-50	BGHcLV22-50	BGHcLV22-50
Sample Name	SART1-BGHcLV22-49	SART1-BGHcLV22-49	SART1-BGHcLV22-49	SART1-BGHcLV22-49	SART1-BGHcLV22-49	SART1-BGHcLV22-49	SART1-BGHcLV22-50	SART1-BGHcLV22-50	SART1-BGHcLV22-50	SART1-BGHcLV22-50
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		SART1-BGHcLV22-49.pdf	L-SART1-BGHcLV22-49.pdf				SART1-BGHcLV22-50.pdf	L-SART1-BGHcLV22-50.pdf
ID	2407	2451	2515	2579	2609	7318	2452	2516	2580	2610

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
SART1-BGHcLV22-49_ACTAAGAT+CCGCGGTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	506	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1372
SART1-BGHcLV22-49_ACTAAGAT+CCGCGGTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	506	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1436
SART1-BGHcLV22-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	506					GRCh38	V40	SART1-BGHcLV22-49_ACTAAGAT+CCGCGGTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SART1-BGHcLV22-49_ACTAAGAT+CCGCGGTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25275
SART1-BGHcLV22-49_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	506					GRCh38	V40	SART1-BGHcLV22-49_ACTAAGAT+CCGCGGTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SART1-BGHcLV22-49_ACTAAGAT+CCGCGGTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25373
SART1-BGHcLV22-49_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	506					GRCh38	V40	SART1-BGHcLV22-49/Aligned.sortedByCoord.out.bam		ENCORE2	26023
SART1-BGHcLV22-49_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	506					GRCh38	V40	SART1-BGHcLV22-49/Aligned.sortedByCoord.out.bam		ENCORE2	26053
SART1-BGHcLV22-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	506					GRCh38	V40	SART1-BGHcLV22-49/Aligned.sortedByCoord.out.bam		ENCORE2	26083
SART1-BGHcLV22-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	506					GRCh38	V40	SART1-BGHcLV22-49/Aligned.sortedByCoord.out.bam		ENCORE2	26113
SART1-BGHcLV22-50_GTCGGAGC+TTATAACC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	507	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1373
SART1-BGHcLV22-50_GTCGGAGC+TTATAACC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	507	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1437
SART1-BGHcLV22-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	507					GRCh38	V40	SART1-BGHcLV22-50_GTCGGAGC+TTATAACC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SART1-BGHcLV22-50_GTCGGAGC+TTATAACC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25276
SART1-BGHcLV22-50_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	507					GRCh38	V40	SART1-BGHcLV22-50_GTCGGAGC+TTATAACC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SART1-BGHcLV22-50_GTCGGAGC+TTATAACC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25374
SART1-BGHcLV22-50_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	507					GRCh38	V40	SART1-BGHcLV22-50/Aligned.sortedByCoord.out.bam		ENCORE2	26024
SART1-BGHcLV22-50_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	507					GRCh38	V40	SART1-BGHcLV22-50/Aligned.sortedByCoord.out.bam		ENCORE2	26054
SART1-BGHcLV22-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	507					GRCh38	V40	SART1-BGHcLV22-50/Aligned.sortedByCoord.out.bam		ENCORE2	26084
SART1-BGHcLV22-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	507					GRCh38	V40	SART1-BGHcLV22-50/Aligned.sortedByCoord.out.bam		ENCORE2	26114